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Molecular Mechanisms of Plant Stress Responses
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Molecular Mechanisms of Plant Stress Responses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 August 2023) | Viewed by 13637

Special Issue Editors

Dr. Malay Das

E-Mail Website
Guest Editor
Department of Life Sciences, Presidency University, Kolkata 700073, India
Interests: osmotic stress; flowering; gene duplication; cellulose; Brassica
Dr. Jianhui Ma

E-Mail Website
Guest Editor
College of Life Science, Henan Normal University, Xinxiang 453007, China
Interests: wheat; transgene; multi-omics; GWAS; physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, abiotic stress has emerged as the major factor limiting crop productivity worldwide. The situation is expected to worsen as global climate change continues to develop. Plants have developed complex strategies to adapt to these stresses. In the past few decades, a number of studies have been conducted to study the regulatory mechanisms in response to major abiotic stresses such as drought, salt, heavy metal and freezing stresses. In addition to identifying important genes, such as NAC, PYL and HXK, the abscisic acid (ABA)-dependent and ABA-independent pathways had been deeply investigated. Additionally, significant progress has been made in identifying advanced phenotyping techniques to detect minute changes with respect to plant growth and development. While substantial progress has been achieved with regard to reference plants, many commercially important crops remained overlooked. This has happened due to many reasons, such as the complexity of polyploid genomes, unavailability of precise genome editing tools, expenses associated with many omics methods, etc. With advancements in technology, the time has come to translate our existing knowledge to crops to develop stress-resilient plants.    

Hence, the aim of this Special Issue is to provide a platform to the researchers who are addressing many of the pertinent issues related to the development of “climate ready crop plants”. Gene function analyses and multi-omics approaches for these analyses are encouraged, but submission are not limited to these methods only.

Dr. Malay Das
Dr. Jianhui Ma
Guest Editors

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Keywords

  • abiotic stress
  • biotic stress
  • phenotyping
  • signalling
  • genome editing
  • transgenic
  • crop plants

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Published Papers (7 papers)

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Research

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16 pages, 2013 KiB  
Article
Identification of Genomic Regions Associated with Seedling Frost Tolerance in Sorghum
by Niegel La Borde and Ismail Dweikat
Genes 2023, 14(12), 2117; https://doi.org/10.3390/genes14122117 - 23 Nov 2023
Viewed by 1198
Abstract
Sorghum bicolor (L.) Moench is the fifth most valuable cereal crop globally. Although sorghum is tolerant to drought and elevated temperatures, it is susceptible to chilling, frost, and freezing stresses. Sorghum seeds planted in April may encounter frequent frost during late April and [...] Read more.
Sorghum bicolor (L.) Moench is the fifth most valuable cereal crop globally. Although sorghum is tolerant to drought and elevated temperatures, it is susceptible to chilling, frost, and freezing stresses. Sorghum seeds planted in April may encounter frequent frost during late April and early May. Early spring freezing temperatures adversely affect crop development and yield. This study aims to identify genomic regions associated with frost tolerance at the seedlings stage. Breeding freeze-tolerant cultivars require selection for freeze tolerance in nurseries. However, the unpredictability of environmental conditions complicates the identification of freeze-tolerant genotypes. An indoor selection protocol has been developed to investigate the genetic determinism of freeze tolerance at the seedling stages and its correlation with several developmental traits. To accomplish this, we used two populations of recombinant inbred lines (RIL) developed from crosses between cold-tolerant (CT19, ICSV700) and cold-sensitive (TX430, M81E) parents. The derived RIL populations were evaluated for single nucleotide polymorphism (SNP) using genotype-by-sequencing (GBS) under controlled environments for their response to freezing stress. Linkage maps were constructed with 464 and 875 SNPs for the CT19 X TX430 (C1) and ICSV700 X M81E(C2) populations. Using quantitative trait loci (QTL) mapping, we identified six QTLs conferring tolerance to freezing temperatures. One QTL in the C1 population and four QTLs in the C2 population, explain 17.75–98% of the phenotypic variance of traits measured. Proline leaf content was increased in response to exposing the seedlings to low temperatures. Candidate QTLs identified in this study could be further exploited to develop frost-tolerant cultivars as proxies in marker-assisted breeding, genomic selection, and genetic engineering. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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19 pages, 5882 KiB  
Article
Comparative Analysis of the GATA Transcription Factors in Five Solanaceae Species and Their Responses to Salt Stress in Wolfberry (Lycium barbarum L.)
by Fengfeng Zhang, Yan Wu, Xin Shi, Xiaojing Wang and Yue Yin
Genes 2023, 14(10), 1943; https://doi.org/10.3390/genes14101943 - 15 Oct 2023
Cited by 1 | Viewed by 1557
Abstract
GATA proteins are a class of zinc-finger DNA-binding proteins that participate in diverse regulatory processes in plants, including the development processes and responses to environmental stresses. However, a comprehensive analysis of the GATA gene family has not been performed in a wolfberry ( [...] Read more.
GATA proteins are a class of zinc-finger DNA-binding proteins that participate in diverse regulatory processes in plants, including the development processes and responses to environmental stresses. However, a comprehensive analysis of the GATA gene family has not been performed in a wolfberry (Lycium barbarum L.) or other Solanaceae species. There are 156 GATA genes identified in five Solanaceae species (Lycium barbarum L., Solanum lycopersicum L., Capsicum annuum L., Solanum tuberosum L., and Solanum melongena L.) in this study. Based on their phylogeny, they can be categorized into four subfamilies (I-IV). Noticeably, synteny analysis revealed that dispersed- and whole-genome duplication contributed to the expansion of the GATA gene family. Purifying selection was a major force driving the evolution of GATA genes. Moreover, the predicted cis-elements revealed the potential roles of wolfberry GATA genes in phytohormone, development, and stress responses. Furthermore, the RNA-seq analysis identified 31 LbaGATA genes with different transcript profiling under salt stress. Nine candidate genes were then selected for further verification using quantitative real-time PCR. The results revealed that four candidate LbaGATA genes (LbaGATA8, LbaGATA19, LbaGATA20, and LbaGATA24) are potentially involved in salt-stress responses. In conclusion, this study contributes significantly to our understanding of the evolution and function of GATA genes among the Solanaceae species, including wolfberry. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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12 pages, 2234 KiB  
Article
Mulberry MnGolS2 Mediates Resistance to Botrytis cinerea on Transgenic Plants
by Donghao Wang, Zixuan Liu, Yue Qin, Shihao Zhang, Lulu Yang, Qiqi Shang, Xianling Ji, Youchao Xin and Xiaodong Li
Genes 2023, 14(10), 1912; https://doi.org/10.3390/genes14101912 - 6 Oct 2023
Viewed by 1348
Abstract
Galactitol synthetase (GolS) as a key enzyme in the raffinose family oligosaccharides (RFOs) biosynthesis pathway, which is closely related to stress. At present, there are few studies on GolS in biological stress. The expression of MnGolS2 gene in mulberry was increased under Botrytis [...] Read more.
Galactitol synthetase (GolS) as a key enzyme in the raffinose family oligosaccharides (RFOs) biosynthesis pathway, which is closely related to stress. At present, there are few studies on GolS in biological stress. The expression of MnGolS2 gene in mulberry was increased under Botrytis cinerea infection. The MnGolS2 gene was cloned and ectopically expressed in Arabidopsis. The content of MDA in leaves of transgenic plants was decreased and the content of CAT was increased after inoculation with B. cinerea. In this study, the role of MnGolS2 in biotic stress was demonstrated for the first time. In addition, it was found that MnGolS2 may increase the resistance of B. cinerea by interacting with other resistance genes. This study offers a crucial foundation for further research into the role of the GolS2 gene. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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18 pages, 6945 KiB  
Article
Brassica rapa Nitrate Transporter 2 (BrNRT2) Family Genes, Identification, and Their Potential Functions in Abiotic Stress Tolerance
by Bingcan Lv, Yifan Li, Xiaoyu Wu, Chen Zhu, Yunyun Cao, Qiaohong Duan and Jiabao Huang
Genes 2023, 14(8), 1564; https://doi.org/10.3390/genes14081564 - 31 Jul 2023
Viewed by 1494
Abstract
Nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO3−) uptake and translocation as well as abiotic stress responses in plants. However, little is known about the NRT2 gene family in Brassica rapa. In this study, 14 [...] Read more.
Nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO3−) uptake and translocation as well as abiotic stress responses in plants. However, little is known about the NRT2 gene family in Brassica rapa. In this study, 14 NRT2s were identified in the B. rapa genome. The BrNRT2 family members contain the PLN00028 and MATE_like superfamily domains. Cis-element analysis indicated that regulatory elements related to stress responses are abundant in the promoter sequences of BrNRT2 genes. BrNRT2.3 expression was increased after drought stress, and BrNRT2.1 and BrNRT2.8 expression were significantly upregulated after salt stress. Furthermore, protein interaction predictions suggested that homologs of BrNRT2.3, BrNRT2.1, and BrNRT2.8 in Arabidopsis thaliana may interact with the known stress-regulating proteins AtNRT1.1, AtNRT1.5, and AtNRT1.8. In conclusion, we suggest that BrNRT2.1, BrNRT2.3, and BrNRT2.8 have the greatest potential for inducing abiotic stress tolerance. Our findings will aid future studies of the biological functions of BrNRT2 family genes. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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15 pages, 3333 KiB  
Article
Comparative Proteomic Analysis of Roots from a Wild Eggplant Species Solanum sisymbriifolium in Defense Response to Verticillium dahliae Inoculation
by Liyan Wu, Min Gui, Jiaxun Liu, Jie Cheng, Zhibin Li, Rui Bao, Xia Chen, Yaju Gong and Guanghui Du
Genes 2023, 14(6), 1247; https://doi.org/10.3390/genes14061247 - 10 Jun 2023
Cited by 4 | Viewed by 1641
Abstract
Eggplant verticillium wilt, caused by Verticillium spp., is a severe eggplant vascular disease. Solanum sisymbriifolium, a wild species of eggplant that is resistant to verticillium wilt, will be beneficial for genetically modifying eggplants. To better reveal the response of wild eggplant to [...] Read more.
Eggplant verticillium wilt, caused by Verticillium spp., is a severe eggplant vascular disease. Solanum sisymbriifolium, a wild species of eggplant that is resistant to verticillium wilt, will be beneficial for genetically modifying eggplants. To better reveal the response of wild eggplant to verticillium wilt, proteomic analysis by iTRAQ technique was performed on roots of S. sisymbriifolium after exposure to Verticillium dahliae, and some selected proteins were also validated using parallel reaction monitoring (PRM). After inoculation with V. dahliae, the phenylalanine ammonia lyase (PAL) and superoxide dismutase (SOD) enzymes and the malondialdehyde (MDA) and soluble protein (SP) of S. sisymbriifolium roots all exhibited an increase in activity or content compared with that of the mock-inoculated plants, especially at 12 and 24 h post-inoculation (hpi). A total of 4890 proteins (47.04% of the proteins were from S. tuberosum and 25.56% were from S. lycopersicum according to the species annotation) were identified through iTRAQ and LC-MS/MS analysis. A total of 369 differentially expressed proteins (DEPs) (195 downregulated and 174 upregulated) were obtained by comparison of the control and treatment groups at 12 hpi, and 550 DEPs (466 downregulated and 84 upregulated) were obtained by comparison of the groups at 24 hpi. The most significant Gene Ontology (GO) enrichment terms at 12 hpi were regulation of translational initiation, oxidation-reduction, and single-organism metabolic process in the biological process group; cytoplasm and eukaryotic preinitiation complex in the cellular component group; and catalytic activity, oxidoreductase activity, and protein binding in the molecular function group. Small molecule metabolic, organophosphate metabolic, and coenzyme metabolic processes in the biological process group; the cytoplasm in the cellular component group; and catalytic activity and GTPase binding in the molecular function group were significant at 24 hpi. Then, KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis was performed, and 82 and 99 pathways (15 and 17, p-value < 0.05) were found to be enriched at 12 and 24 hpi, respectively. Selenocompound metabolism, ubiquinone, and other terpenoid-quinone biosyntheses, fatty acid biosynthesis, lysine biosynthesis, and the citrate cycle were the top five significant pathways at 12 hpi. Glycolysis/gluconeogenesis, biosynthesis of secondary metabolites, linoleic acid metabolism, pyruvate metabolism, and cyanoamino acid metabolism were the top five at 24 hpi. Some V. dahliae-resistance-related proteins, including phenylpropanoid-pathway-related proteins, stress and defense response proteins, plant–pathogen interaction pathway and pathogenesis-related proteins, cell wall organization and reinforcement-related proteins, phytohormones-signal-pathways-related proteins, and other defense-related proteins were identified. In conclusion, this is the first proteomic analysis of S. sisymbriifolium under V. dahliae stress. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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15 pages, 12498 KiB  
Article
Comprehensive Transcriptome Analysis of Responses during Cold Stress in Wheat (Triticum aestivum L.)
by Lei Li, Chenglin Han, Jinwei Yang, Zhiqiang Tian, Ruyun Jiang, Fei Yang, Kemeng Jiao, Menglei Qi, Lili Liu, Baozhu Zhang, Jishan Niu, Yumei Jiang, Yongchun Li and Jun Yin
Genes 2023, 14(4), 844; https://doi.org/10.3390/genes14040844 - 31 Mar 2023
Cited by 7 | Viewed by 2901
Abstract
Wheat production is often impacted by pre-winter freezing damage and cold spells in later spring. To study the influences of cold stress on wheat seedlings, unstressed Jing 841 was sampled once at the seedling stage, followed by 4 °C stress treatment for 30 [...] Read more.
Wheat production is often impacted by pre-winter freezing damage and cold spells in later spring. To study the influences of cold stress on wheat seedlings, unstressed Jing 841 was sampled once at the seedling stage, followed by 4 °C stress treatment for 30 days and once every 10 days. A total of 12,926 differentially expressed genes (DEGs) were identified from the transcriptome. K-means cluster analysis found a group of genes related to the glutamate metabolism pathway, and many genes belonging to the bHLH, MYB, NAC, WRKY, and ERF transcription factor families were highly expressed. Starch and sucrose metabolism, glutathione metabolism, and plant hormone signal transduction pathways were found. Weighted Gene Co-Expression Network Analysis (WGCNA) identified several key genes involved in the development of seedlings under cold stress. The cluster tree diagram showed seven different modules marked with different colors. The blue module had the highest correlation coefficient for the samples treated with cold stress for 30 days, and most genes in this module were rich in glutathione metabolism (ko00480). A total of eight DEGs were validated using quantitative real-time PCR. Overall, this study provides new insights into the physiological metabolic pathways and gene changes in a cold stress transcriptome, and it has a potential significance for improving freezing tolerance in wheat. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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Review

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23 pages, 1548 KiB  
Review
GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms
by Ling Liu, Yuxin Xie, Baba Salifu Yahaya and Fengkai Wu
Genes 2024, 15(1), 94; https://doi.org/10.3390/genes15010094 - 13 Jan 2024
Cited by 2 | Viewed by 2348
Abstract
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian [...] Read more.
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants’ adaptability to environmental challenges. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Responses)
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